Claudia and Paracelsus, the two caretakers of the Warehouse 13, face off against each other. Paracelsus uses his control of the warehouse to throw a fireball at Claudia, who transforms it into ice. She fires a Tesla at him but he absorbs the energy and throws a Japanese fan at her, breaking a shelf as she ducks aside. He then fires a cannon at her and Claudia stops it with a gesture. She points out that she's part of the warehouse and it won't let him kill her, and she draws a warehouse. However, Paracelsus realizes that he can control her if he controls the warehouse and takes control of her body.
Paracelsus has Claudia lead him to the office and probes her memories. Once he's done, Paracelsus says that they have a lot in common. He has her bring up information on Karl Schwarzschild and explains that Claudia is going to help him combine a few artifacts that will change everything.
Myka is at the hospital after surgery and the doctor tells her to take care. Pete comes in to check on her and she dismisses the doctor. As soon as the doctor is gone, Myka gets up and Pete wonders if she's good. His partner tells him that the cyst was benign and asks how things are going at the warehouse.
Outside the warehouse, Artie dumps purple neutralizer goo on their rental car and tells Steven to back up and drive through the force field that Paracelsus erected. As Steven backs up, Mrs. Frederic calls Artie to tell him that she's on her way to meet with the Regents, who are on an overseas retreat. Artie assures her that there's nothing to worry about and signs off, just as Steven slams the rental into the force field and comes to an abrupt stop. Steven says that they should wait for Pete and Myka to come back, and Artie says that he has another idea and heads off for a crowded parking lot.
As they get in their car, Pete brings Myka up to speed on Paracelsus but avoids explaining that he inadvertently freed him by trying to cure Myka. When Pete mentions the shield, Myka says that they need to get to the Innes Observatory right away.
Artie returns to the warehouse with a bunch of car batteries and rigs them all together. Steven wonders how they're going to stop Paracelsus and Artie tells him that they'll use the arrow artifact that killed Achilles. They attach the jumper cables to the force field and Steve gets blasted back. Pete and Myka arrive and Myka explains that the shield draws power from the Alpha Centauri star system. After Sykes used the force field against them, the Regents installed a failsafe at the Innes Observatory. Myka redirected the laser scope to Uranus, letting them pass through it. She strikes through the barrier and the others follow her in.
Inside, Artie explains that he knows a way to disconnect Paracelsus from the warehouse, but he'll need someone to help him. Myka goes with him while Pete and Steven create a diversion. Pete starts knocking things over and calls to Paracelsus. In the office, he senses them and sends Claudia with a missile launcher. They run for it and Claudia grabs Al Capone's machineguns guns and shoots at them.
Artie and Myka go to the Eldunari and Artie explains that they have to put the fires back in the alcoves and redo the Nordic symbols containing them. He takes out a set of artifact mirrors and uses them to reflect the flames into the alcoves, reigniting them and disconnecting Paracelsus. Artie warns that the flames will consume them if they don't do it simultaneously. After Myka pauses to sneeze, Artie uses the mirrors and their plan works... to reignite two of the alcoves.
Claudia corners Pete and Steve and prepares to shoot them with a crossbow.
Artie tell Myka to wait... and the other two alcoves finally ignite. Paracelsus loses control of the warehouse and Claudia, but realizes that it doesn't matter and goes back to work. Meanwhile, the two groups make contact via Farnesworth and Claudia explains that Paracelsus is attaching various artifacts to H.G. Wells' time machine at the portal. All of the artifacts are science-related and extremely powerful, and they figure that Paracelsus is planning a trip. Artie tells them to get the arrow and some guns while he and Myka pick something else up.
Paracelsus activates the time machine and the attached artifacts, and creates a physical portal. He laughs in triumph just as Pete arrive and shoots, but misses. Paracelsus tells them that he will create a new world order and leaps into the portal. Myka and Artie arrive and toss the others metal forks, just as waves of energy sweep through the warehouse. It transforms into a totally different building and they find pictures of Paracelsus on banners representing the last five warehouses. They realize that Paracelsus was the caretaker of the warehouses
The group takes in the banners and Artie concludes that Paracelsus hasn't significantly changed history. The motto on the banner partially reads, "Science is everything," and they realize that the warehouse is focused entirely on science. Artie explains that the fork artifacts are embued with the power to maintain the holder in their original time continuum. Claudia accesses an advanced computer terminal and a hologram of Paracelsus appears. They realize that it's a computer guide program, and Claudia makes it disappear. The rest of the motto reads "The end justifies the means." Claudia says that she'll need to get to the hub to access the computer system. When Artie says that they need her to recreate the time portal, Claudia disagrees and reminds him about how he concealed the existence of her sister from her.
Claudia and Pete follow the fiber optic connections and Pete asks what is going on between her and Artie. Before she can explain, troopers march by wearing artifact mind-control lenses and Spines of Saracens. Pete realizes that Paracelsus is recreating artifacts. Benedict Valda arrives, alive in the current timeline, and confirms that the troopers are following commands. Once they leave, Claudia and Pete move on.
Artie, Myka, and Steven set up the time machine and look for the three artifacts. They hear someone screaming from a nearby room and go in, and find two scientists experimenting on a man with two artifacts. Artie closes the screen and remembers what his parents used to tell him about the concentration camps during World War II.
Claudia and Pete go the central computer room and find Abigail tied into the center of the machine. They realize that she's tied into the computer and Paracelsus is using her brain to augment the processing functions. Claudia tries to access the classified information without success and then starts checking the low-level info.
Artie and the others find the three artifacts and realize that the Tesla power source may not be sufficient to send Pete and Myka back once Claudia finds out where they need to go. An alarm goes off as they move around the artifact, just as Pete and Claudia arrive and tell them that the target date is June 10, 1541. Claudia figures that she went to Warehouse 9 because the Regents were killed at that date. After that, Paracelsus ran the warehouse without supervision.
With time running out, they activate the mechanisms and the portal opens. Troopers march toward them and Artie runs off to distract them while Claudia and Steven keep the portal open so Pete and Myka can go through. Claudia goes after her friend and sees the troopers haul Artie away, while Pete and Myka enter the portal.
The two agents find themselves in a mausoleum surrounded by dead guards. One of them has the Arrow of Achilles in him that Pete fired earlier. Myka arrive first and by the time Pete comes through, a woman has captured Myka and holds a knife to her throat. Pete introduces himself and the woman explains that she's Lisa DaVinci, agent of Warehouse 9. She explains that she's Leonardo's granddaughter, and Pete tells her that they're time travelers. Lisa tells them that she's been working on time travel for 40 years and wonders what took them for so long. Myka manages to disarm Lisa and tells her that Paracelsus killed the men. Lisa tells them that Paracelsus was imprisoned in bronze that very day.
Artie is taken to Valda for experimentation, and Valda doesn't believe Artie's claims of alternate timelines. Paracelsus comes in and realizes that it's the day that he changes everything. He doesn't believe Artie when he claims that he's there by his own, and tells Valda to start using artifacts to jog his memory. Doctors Vanessa Calder and Hugo Miller come in to work on their new subject.
Steven and Claudia do what they can to keep feeding power to the time portal. They rig up Jack LaLanne's stationary bike and Steven rides it to provide power while Claudia goes to save Artie.
Artie tries to convince Vanessa and Hugo that they are friends in an alternate reality. Hugo explains that they're married, and they loudly insist that they're working for the benefit of humanity as they glance at the security cameras. Artie realizes that they're afraid of Paracelsus and they finally explain that Paracelsus has their children. As they prepare to experiment on him, Artie recites personal information about them that only their closest friends could know.
Lisa gets a mirror out of storage that will let them see the immediate future, while the agents explain what happened. They watch as Paracelsus emerges from the time portal and kills the guards, using the Arrow of Achilles on the first one and his sword on the others. Lisa is satisfied that the agents are telling the truth and informs them that the Regents are meeting that very day to appoint a caretaker to replace Paracelsus. She doesn't know where they meet, but Pete figures that they meet in public everyday places. He rattles off a list of 21st century places, and Lisa realizes that they'll be at the olive garden.
Claudia overhears Paracelsus and Valda talking, and Paracelsus hesitates briefly before going to check on the artifacts.
Vanessa tells Artie that they have no choice but to experiment on him. As they get out the artifacts, Claudia uses her Tesla to stun them and points out that it's heartbreaking when good friends turn against someone. Artie insists that he's still the same man he always was and was trying to protect her, but Claudia says that he can't protect her anymore. Paracelsus addresses them from the observation chamber and says that they won't be protecting anyone anymore, and Valda and a trooper come in.
At the olive garden, the Regents are discussing who to assign as next caretaker. The future Paracelsus arrives and tells them that their guards are dead. He explains that he plans to lead the warehouse into a future of science as the one true faith. Paracelsus asks if they're with him or against him and they refuse to work with him. He then drives an elephant tusk artifact into the ground, crushing them with monstrous boa constrictors. Pete, Myka, and Lisa arrive and Lisa whistles. Paracelsus runs off and a purple swamphen flies down. It grabs the artifact and flies off, freeing the Regents. Myka figures that Paracelsus is heading back to Warehouse 9 to link up with the Eldunari and take control, and runs off there with Pete and Lisa.
The soldiers strap Claudia into a chair next to Artie. The scientists bring out Alice's mirror, clearly unaware of what it really does, and Artie asks Vanessa and Hugo to take a picture of them first.
When they get to the warehouse, the three agents find another dead guard. Pete heads for the Eldunari while Myka and Lisa circle around.
At the time portal, the intruder alarms go off and Steven draws his guns.
In 1541, Pete finds Paracelsus searching for artifacts. He tosses a marble at Pete which explodes into more flaming balls. Pete climbs up a ladder onto the shelves and continues his pursuits. He gets ahead of Paracelsus and throws a scalpel into his leg.
In the altered present, Paracelsus and Valda are going to investigate the alarm when Paracelsus suddenly clutches at his leg.
Pete tackles Paracelsus.
In the present, Paracelsus tells Valda to stay behind while he deals with the intruder.
As he pins Paracelsus, Pete reminds him of how he dangled Myka's life in front of him. Pete is unaware that Lisa and Myka have arrived and can hear what he's saying. Paracelsus begs for the chance to alter the future, but Pete drags him off to the bronze section.
In the present, Paracelsus enters the room with the time portal and easily disarms Steven. As he prepares to kill the agent with another artifact, time resets and everything reverts to normal.
Once everyone is back together, Claudia confirms that Mrs. Frederic is back online and in charge of the warehouse. She says that something is changing but she can't explain what. Abigail says that the Regents have asked her to meet them aboard. Pete leads the group to a sarcophagus where they locked up "their" bronzed Paracelsus. Artie tells Pete to take Paracelsus to the Bronze Sector and takes off with the others. Myka stays back and asks Pete why he had the scalpel. She knows that it had curative properties and figures that he brought it to Paracelsus to cure her. Pete finally admits that he did and Myka tells him never to endanger the warehouse and the world for her.
As Artie puts the forks back, he congratulates Claudia on her idea with Alice's mirror. Claudia says that she hasn't forgotten her sister Claire and walks off, while Artie realizes that one of the forks is missing.
Elsewhere in the warehouse, the alternate Valda opens his counterpart's room in the Personnel Quarters Archive, tapping the fork on the control panel.